Thursday, November 27, 2008

Well, it is Thanksgiving. I am up late as usual catching up on email. On this day, there is something I have been meaning to post for a few years. I think scientists should take a breath today and give thanks to those who have helped them along the way. I have some specific postings about this in terms of who I want to thanks, but I wanted to make a list here of the types of things scientists should be thankful for. So here goes.

10 things scientists should be thankful for

Teachers. Scientists had to learn science at some point. And most of us have had some stellar science teachers, or teachers of science-related things like math, along the way. We should give thanks to these people.

Inspirers. Similar to #1 except in many cases we have been inspired to become scientists by someone who may not have been a teacher of ours. Perhaps it was a famous scientist, or even a fictional one. Or even someone we knew. It is that inspiration that frequently gets one through the tough times.

Benefactors In general, scientists have a pretty nice life. We get paid (sometimes well, sometimes poorly) and are given research funds, to unlock the secrets of the universe. How cool is that? We should therefore be very thankful for the immediate source of our funds - such as the institutes where we work and the agencies that provide us funds.

Taxpayers. Unless one is funded by private foundations, taxpayers are the ultimate source of those funds mentioned in #3. This source of funds is frequently overlooked but should never be forgotten. Don't forget - we take money people from people that in theory they could have gotten to keep if their taxes were lower. We should thank these taxpayers..

Research personnel (including student researchers, post docs, technicians, etc). Most of the time, scientists get credit for some work that was in a large part actually done by people in our labs. They deserve our eternal gratitude.

Students we teach. Overall, for those scientists who teach, though it may be a required part of our jobs, it is also a great way to learn and to become a better scientist.

Staff at publishers. An important part of communicating science is of course publishing. And though I am a big fan of new ways to disseminate information, let us not forget that there are many many people who aid and abet this dissemination by working for publishers. These folks deserve our thanks.

Study subjects or objects. Whether one studies organisms, rocks, molecules, planets, forces, or whatever, we should all be thankful that there is interesting stuff out there to study. And for those who study living things, if one disturbs them along the way, we should

Librarians and library staff. Access to information is critical for both learning to become a scientist and being a scientist. And libraries play a key role in providing this access.

Family and friends. Late nights at the lab? Working on a grant over the weekend? Writing papers all the time? In school for years and years? All of this takes a toll on friends and family. And we owe them some props.

I am sure there are more categories. But these are some that came to me on this Thanksgiving. Any categories I missed?

Wednesday, November 26, 2008

For all out there who love ciliates and their relatives, you might want to check out the second paper to come out of my Tetrahymena thermophila Genome Sequencing Project for which the preprint is available in BMC Genomics.

In this project we have been sequencing, annotating and finishing the macronuclear genome of this lovely organism. Like other ciliates Tetrahymena has two nuclei and two nuclear genomes - the macronucleus (MAC) and the micronucleus (MIC). The MIC is analogous to germ cells in animals -- it is sort of a genomic repository for sexual reproduction. After sexual reproduction, the MIC genome is processed to generate the MAC genome which is then used in an analogous way to soma cells in animals (the MAC is the site for most/all gene expression in Tetrahymena). I have been the PI on this project which was supported by grants from NSF and NIH and was a collaboration involving TIGR (where I used to work), Stanford, UCSB, JCVI (which subsumed TIGR a few years ago) and the Tetrahymena research community.

The new paper describes further work on the MAC genome including finishing many of the chromosomes (which was done spectacularly by Luke Tallon and Kristie Jones), sequencing and analyzing a larger number of ESTs, refining the annotation (coordinated by Mathangi Thiagarajan), and some other analyses. The new paper was led by Bob Coyne, who, with Barb Methé took over coordinating the work at TIGR/JCVI after I moved to UC Davis a few years back. I think they did a stellar job (ni biases here).

Note - I took the title of the posting 'Tackling a Hairy Best" from an NIH press release that was put out when we got the grants for this project.

Of course I am a bit biased I suppose as I am heavily involved in PLoS and also served as Academic Editor for these papers. But with that being said, I encourage people to check them out. In the PLoS Genetics paper from the labs of Mitch Sogin and David Relman labs discusses continued development of the use of 454-Roche pyrosequencing technology to carry out deep rRNA sampling. Anybody interested in characterizing a microbial community deeply in terms of what organisms are there should consider this approach.

And in the second paper, the same two labs present an in depth study using the 454-Roche rRNA sequencing to characterize the response of microbes in the human gut to antibiotic treatment. Though there have been a few other such studies this is the one that has the deepest characterization of the microbes present.

Note - one thing I find kind of humorous is that one of the authors is listed as Susan M. Huse in one of the papers (she is the first author on the PLoS Genetics paper) and Sue Huse in the other.

Friday, November 21, 2008

Quick post here. Cool new paper (and the software could be cool too but have not tried it yet) on simulating genome evolution. The paper is from Ian Holmes and others at Berkeley (see his lab page on BioWiki here) and the paper can be found here in Genome Biology. Here is the abstract:

Controlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three new open-source programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic structured features) and SIMGENOME (for syntenic genome blocks). Each offers algorithms for parameter measurement and reconstruction of ancestral sequence. All three tools out-perform the leading neutral DNA simulator (DAWG) in benchmarks. The programs are available at http://biowiki.org/SimulationTools.

I may see PLoS even when it is not there, but in this picture, which was the group photo for the Metagenomics 2008 meeting at CalIT2, I weaseled my way to the front hoping to get my PLoS bag and PLoS shirt into the picture. And looky there - it worked.

As a Boston native, one of the worries I had moving out to Davis a few years ago related to being too far from the RedSox, Sure they come to Oakland and sure my brother has season tickets to the A's mostly to get RedSox tickets, but California is really far from Fenway Park. Well, at least there are lots of RedSox fans around here, especially if I go up to Woodland. Woodland, if you do not know, is the home town of the newest RedSox superstar, Dustin Pedroia, who nearly carried the Sox into the World Series and today was awarded the American League MVP Award. Way to go Dustin and thanks Woodland for helping out my team.

I am starting a new thread here - microbiology in the news. And my first posting is about bleach. Everyone probably has used it at one time or another to clean something. And some people use it to kill "germs" (aka microbes) too. Well, MSNBC is reporting (Mystery solved: How bleach kills germs - Science- msnbc.com) on a Cell article that presents evidence regarding how the active ingredient in bleach (hypochlorous acid) kills bacteria. Apparently, it works in a similar way to heat in destabilizing protein structures. Anyway, the researchers claim that this is relevant to killing of microbes inside of people because

"Hypochlorous acid is an important part of host defense," Jakob said. "It's not just something we use on our countertops."

Whether this is true or not, I do not know. But what I do know is that microbes are in the news. And that is good.

one of eight Bioinformatics Resource Centers (BRC) for Biodefense and Emerging/Re-Emerging Infectious Diseases. Funded by the National Institute of Allergy and Infectious Diseases (NIAID), ERIC serves as an information resource for five members of the bacterial family Enterobacteriaceae.

So if you want to learn more about E. coli and its relatives and their genomes, this is a good place to start

The scientists will focus on marine viruses and other tiny life called protists and their roles in the food chain. These organisms prey on bacteria, a primary food that sustains the vent ecosystem.

Some friends/colleagues of mine are involved in this adventure and it sounds like some cool stuff could come out of it. Also you might want to check out the blog of Lisa Z (ExtremeVirus), who is posting about the cruise.

A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution....

"Our new theory extends Darwin's model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness."

"What we have found is that certain kinds of biological structures exist that are able to steer the process of evolution toward improved fitness,"....Unlike Darwin, Wallace conjectured that species themselves may develop the capacity to respond optimally to evolutionary stresses. Until this work, evidence for the conjecture was lacking....."In this paper, we present what is ostensibly the first quantitative experimental evidence, since Wallace's original proposal, that nature employs evolutionary control strategies to maximize the fitness of biological networks,"

It sounds like complete nonsense to me. But I am not sure. Anyone else out there know more?

Wednesday, November 12, 2008

I do not normally write too much here about non Open Access publications but this one is so good I had to. Everyone with access to Trends in Microbiology should check out Julian Parkhill's rebuttal to an article written by David Whitworth in the same issue. Whitworth's article is "Genomes and knowledge – a questionable relationship? " and it is in my opinion, filled with some unsuppoerted and over the top statements. In essence, he is arguing that we should stop genome sequencing because there are a bunch of genomes out there already and after all, all that matters is work on model organisms so if you have enough genomes related to your model organism you should move on. Alas I do not have time to detail them here. But fortunately, Parkhill does a great job of responding in his article Time to remove the model organism blinkers. The end of his article reflects how I feel too:

In the end, when faced with the astonishing diversity of microorganisms, if all we manage to do is to describe a few random organisms in painstaking detail, then we will have failed to understand microbiology. To suggest we curtail the remit of microbial genomics is bad enough; to suggest it now, when we are on the brink of finally being able to truly study genomic diversity, is absurd.

So sure, sometimes we in genomics oversell the benefits of genome sequence data (and in fact, I give out a little award here for those people). But Whitworth is at the other end of the spectrum, wearing, as Parkhill states "blinkers" to the benefits of genome sequence data. As a reflection of how much I disagree with most of Whitworth's implications, I am giving him my first "Underselling Genomics Award".

Well, just adding my two cents to the pissed off blogosphere regarding a company in Singapore called DNA Dynasty. Not only are they purveying complete crap in terms of genetics/genomics (e.g., they say they have a genetic test to determine the innate abilities of your children) but they have apparently stolen the logo of the DNA Network of which I am a member. Lovely. I figure, if we make enough blogging noise, then when people search for them with google they will at least also see some of our postings. So here is mine. See also

Wednesday, November 05, 2008

#2 - mooched a ride this morning to the conference site from some of the folks who run "The Seed" and related annotation and analysis servers. I have written about them before but people really should check them out if you are interested in microbial genome analysis.

#3 - Alex Worden is talking now about picoeukaryotes. Alex does some of the coolest environmental microbiology out there and just happens to focus on groups of organisms that are frequently ignored. She just said a key quote "Physiology is not a bulk or an average property" basically saying what I say which is that an environment is not simply a bag of genes. That is we need to remember that there are real compartments in communities. Alex just showed an interesting figure on rRNA sampling of uncultured eukaryotes from the Sargasso See (Not et al. EM 2007). Another key point she has made is that microbial eukaryotes are barely sampled in terms of genomics

#4 - a ridiculously short break (the organizers of this meeting really really need to change the scheduling to have more time to talk to people in breaks).

#5 - Oded Beja is talking now. He is really one of the key people behind the entire metagenomics revolution as he was the lead on many of the papers from the Delong Lab onthe discovery of proteorhodopsin

#6 - Shannon Williamson is showing an incredibly cool contraption that she uses to take water samples and size fractionate them in the bottom of the ocean. It is basically a series of filter systems that works on a platform that is run by a deep sea submersible ... this allows them to sample large volumes of water in the deep sea (larger volumes than they could bring back up to the surface)

#7 - a little note --- already many talks referring to using IMG, IMG/M and MG-RAST tools to help with annotation and analysis of genomes and metagenomes. Clearly there is enormous demand for getting ones data analyzed by some public or semi-public tools ...

#8 - Yuri Gorby --- gave a talk about nanowires which are basically little mini cables that cells use to connect to other cells and shuttle electrons around. This stuff is beyond cool --- it is completely fascinating.

Tuesday, November 04, 2008

Well, I apologize but I am not going to post anything today about the metagenomics meeting in San Diego since I came late today as I wanted to be at home for the beginning of the election. But I made my way down to San Diego and made it to dinner. The dinner "entertainment" was a talk by one of the grand gurus of ocean microbiology - Steven Giovannoni. Alas, even he realized that he was competing with people wanting to know about the election and I confess I spent most of his talk hitting reload on my phone and surfing between sites. But So I have no notes to post about his talk. But I can say that I am happy about the election. And tomorrow I will try to post some notes about talks. But I may be still too happy to take notes ...

((Note added later --- in retrospect, I (and others I talked to) felt Steve G's talk had way way too much detail for an after dinner talk so I spent the next day taking out much of the detail from my talk to lighten it up. What did this get me? After my talk and later after drinks Steve G. made it clear he thought it stunk because it was too light on details of something he thought should have been in it. Oh well, I guess this goes to show you cannot make everyone happy.)).

Monday, November 03, 2008

Charles Darwin has again spoken from the grave. In February I reported how Darwin endorsed Obama in the primary against Hilary Clinton (The Tree of Life: Charles Darwin Endorses Obama as the "Natural Selection") (note - his candidacy took off immediately after the 2/5 endorsement). And Darwin is getting in his own November surprise for the election tomorrow. Darwin spoke through a variety of media (I am using this term in reference to the plural of medium - people who speak to the dead .. but I am not sure whether media or mediums is the plural) and said

"This one is such a complete no brainer. Obama is so far and away the fitter candidate. Plus if Palin and McCain do not believe in my greatest work, well they can ..." (we cannot print the rest)

So there it is. Of course, most living well known scientists who have made public statements also endorse Obama, but getting Darwin's support is an extra feather in his cap.